Using DNA to predict externally visible characteristics in humans for forensic use in New Zealand

Abstract

The ability to predict externally visible characteristics (EVCs) from DNA has appeal for use in forensic science, particularly where a forensic DNA profile database match is not made and an eye witness account is unavailable. This technology has yet to be implemented in casework in New Zealand. The broad cultural diversity of New Zealand dictates that any EVC predictions made using anonymous DNA must perform accurately in the absence of knowledge of the donor’s ancestral background. Here we investigate SNP association with hair and eye colour phenotypes. An initial screening set of nineteen SNPs from ten different known or suspected pigmentation genes were selected from the literature. Seventeen SNPs were screened for phenotype association with genotypes derived from one hundred and one unrelated individuals from different ancestral backgrounds. Classification tree recursive partitioning was used to model SNP collectively against phenotype. Alternate models capable of predicting eye colour from the DNA genotypes of SNPs located within the HERC2, OCA2, TYR and SLC24A4 genes using probability calculation and classification trees. The final model selected for eye colour prediction exhibited high levels of accuracy for both blue (89%) and brown eye colour (94%). Brown hair colour was predicted accurately using a single SNP from the HERC2 gene, although hair colour models require further development using a larger dataset and a greater number of SNPs. A multiplex assay was designed to include the SNPs required for eye colour prediction. Genetic markers for Y chromosome DNA were integrated into this assay as a secondary gender test, following typical DNA profiling. Three genes specific to the Y chromosome were applied as four different markers used to indicate the presence of Y chromosome DNA within a sample and infer a male contributor. Absence of these markers indicates a female contributor. The multiplex was optimised for forensic use and assessed for performance specificity and reproducibility. Finally, this method applied to a blind testing dataset (phenotypes anonymous to researcher) to simulate final use in a forensic setting. Blue and brown eye colour prediction was highly accurate, and all samples were correctly inferred as male and female individuals.